rs6833943

Variant names:

• chr4-157630147-C-T
• rs6833943
• ENST00000652341.2:n.562+47080G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652341.2(ENSG00000286133):​n.562+47080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,970 control chromosomes in the GnomAD database, including 18,891 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (18891 hom., cov: 32)
• Consequence: ENSG00000286133 ENST00000652341.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446

Genes affected

ENSG00000286133 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286133	ENST00000652341.2	n.562+47080G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69224 AN: 151852 Hom.: 18886 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.489

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.456 AC: 69230 AN: 151970 Hom.: 18891 Cov.: 32 AF XY: 0.467 AC XY: 34654 AN XY: 74276

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.496

Alfa AF: 0.513 Hom.: 3711

Bravo AF: 0.445

Asia WGS AF: 0.614 AC: 2135 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6833943; hg19: chr4-158551299;